Strain identifier
BacDive ID: 14128
Type strain:
Species: Sphingobacterium composti
Strain Designation: 4M24
Strain history: KACC 11313 <-- H.-Y. Weon 4M24.
NCBI tax ID(s): 415956 (species)
General
@ref: 7741
BacDive-ID: 14128
DSM-Number: 18850
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Sphingobacterium composti 4M24 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from cotton waste compost.
NCBI tax id
- NCBI tax id: 415956
- Matching level: species
strain history
@ref | history |
---|---|
7741 | <- S.-W. Kwon, KACC <- Yoo et al.; 4M24 |
67770 | KACC 11313 <-- H.-Y. Weon 4M24. |
doi: 10.13145/bacdive14128.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Sphingobacterium
- species: Sphingobacterium composti
- full scientific name: Sphingobacterium composti Yoo et al. 2007
@ref: 7741
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Sphingobacterium
species: Sphingobacterium composti [homonym]
full scientific name: Sphingobacterium composti [homonym] Yoo et al. 2007
strain designation: 4M24
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32089 | negative | 1.5 µm | 0.55 µm | rod-shaped | no | |
69480 | no | 93.586 | ||||
69480 | negative | 99.995 |
pigmentation
- @ref: 32089
- production: yes
Culture and growth conditions
culture medium
- @ref: 7741
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7741 | positive | growth | 28 | mesophilic |
32089 | positive | growth | 10-45 | |
32089 | positive | optimum | 27.5 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32089 | positive | growth | 06-09 | alkaliphile |
32089 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32089
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32089 | no | |
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32089 | NaCl | positive | growth | 0-5 % |
32089 | NaCl | positive | optimum | 2.5 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32089 | 22599 | arabinose | + | carbon source |
32089 | 17057 | cellobiose | + | carbon source |
32089 | 28757 | fructose | + | carbon source |
32089 | 33984 | fucose | + | carbon source |
32089 | 28260 | galactose | + | carbon source |
32089 | 17234 | glucose | + | carbon source |
32089 | 17716 | lactose | + | carbon source |
32089 | 17306 | maltose | + | carbon source |
32089 | 37684 | mannose | + | carbon source |
32089 | 28053 | melibiose | + | carbon source |
32089 | 506227 | N-acetylglucosamine | + | carbon source |
32089 | 16634 | raffinose | + | carbon source |
32089 | 17814 | salicin | + | carbon source |
32089 | 17992 | sucrose | + | carbon source |
32089 | 27082 | trehalose | + | carbon source |
32089 | 53424 | tween 20 | + | carbon source |
32089 | 53426 | tween 80 | + | carbon source |
32089 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32089 | acid phosphatase | + | 3.1.3.2 |
32089 | alkaline phosphatase | + | 3.1.3.1 |
32089 | catalase | + | 1.11.1.6 |
32089 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
7741 | cotton waste compost | Republic of Korea | KOR | Asia |
67770 | Cotton-waste composts | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | |
#Engineered | #Biodegradation | #Composting |
#Engineered | #Waste | #Solid plant waste |
#Host | #Plants | #Shrub (Scrub) |
taxonmaps
- @ref: 69479
- File name: preview.99_67864.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_29308;97_36949;98_47815;99_67864&stattab=map
- Last taxonomy: Sphingobacterium composti subclade
- 16S sequence: EF122436
- Sequence Identity:
- Total samples: 1994
- soil counts: 427
- aquatic counts: 360
- animal counts: 989
- plant counts: 218
Sequence information
16S sequences
- @ref: 32089
- description: Sphingobacterium composti Yoo et al. 2007 strain 4M24 16S ribosomal RNA gene, partial sequence
- accession: EF122436
- length: 1487
- database: nuccore
- NCBI tax ID: 415956
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 strain DSM 18850 | 415956.3 | wgs | patric | 415956 |
66792 | Sphingobacterium composti DSM 18850 | 2700988711 | draft | img | 415956 |
67770 | Sphingobacterium composti Yoo et al. 2007 non Ten et al. 2007 DSM 18850 | GCA_008124885 | scaffold | ncbi | 415956 |
GC content
@ref | GC-content | method |
---|---|---|
32089 | 42.3 | |
67770 | 42.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.133 | no |
anaerobic | no | 98.418 | yes |
halophile | no | 89.819 | no |
spore-forming | no | 96.478 | no |
glucose-util | yes | 92.25 | yes |
aerobic | yes | 85.525 | no |
flagellated | no | 95.041 | yes |
motile | no | 91.693 | yes |
thermophile | no | 97.554 | yes |
glucose-ferment | no | 90.549 | no |
External links
@ref: 7741
culture collection no.: DSM 18850, KACC 11313, JCM 16391, NBRC 106383
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17625199 | Sphingobacterium composti sp. nov., isolated from cotton-waste composts. | Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, Stackebrandt E | Int J Syst Evol Microbiol | 10.1099/ijs.0.64948-0 | 2007 | Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gossypium/microbiology, Korea, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil, *Soil Microbiology, Sphingobacterium/chemistry/*classification/genetics/*isolation & purification | Genetics |
Phylogeny | 18768611 | Sphingobacterium anhuiense sp. nov., isolated from forest soil. | Wei W, Zhou Y, Wang X, Huang X, Lai R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65864-0 | 2008 | Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingobacterium/*classification/genetics/*isolation & purification/physiology, Temperature, *Trees | Genetics |
Phylogeny | 24052628 | Sphingobacterium arenae sp. nov., isolated from sandy soil. | Jiang S, Chen M, Su S, Yang M, Li A, Zhang C, Lin M, Zhang W, Luo X | Int J Syst Evol Microbiol | 10.1099/ijs.0.051706-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silicon Dioxide, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 25201914 | Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert. | Zhao P, Zhou Z, Chen M, Lin W, Zhang W, Wei G | Int J Syst Evol Microbiol | 10.1099/ijs.0.064246-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7741 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18850) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18850 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32089 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28335 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 |